5-107141872-T-G

Variant names:

• chr5-107141872-T-G
• rs1895225

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.475 in 151,072 control chromosomes in the GnomAD database, including 17,254 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.48 (17254 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.475 AC: 71778 AN: 150954 Hom.: 17248 Cov.: 31

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.475

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.475 AC: 71820 AN: 151072 Hom.: 17254 Cov.: 31 AF XY: 0.475 AC XY: 35075 AN XY: 73832

African (AFR) AF: 0.470 AC: 19434 AN: 41334

American (AMR) AF: 0.469 AC: 7106 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1657 AN: 3456

East Asian (EAS) AF: 0.689 AC: 3540 AN: 5140

South Asian (SAS) AF: 0.438 AC: 2106 AN: 4810

European-Finnish (FIN) AF: 0.490 AC: 5154 AN: 10516

Middle Eastern (MID) AF: 0.475 AC: 135 AN: 284

European-Non Finnish (NFE) AF: 0.465 AC: 31317 AN: 67370

Other (OTH) AF: 0.473 AC: 989 AN: 2090

Alfa AF: 0.456 Hom.: 2075

Bravo AF: 0.475

Asia WGS AF: 0.559 AC: 1930 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.75
PhyloP100		-0.044

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1895225; hg19: chr5-106477573; COSMIC: COSV60178301;